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Re: How will low grades in these math courses affect my chances at top masters/PhD/RA
in terms of being competitive for an RA position--your grades are fine. I had very imperfect grades and I got multiple RA offers at top-5 programs. In my experience, professors cared a lot more about previous research experience and programming skills than my grade in some random math class.
since I haven't gone through the phd application cycle I can't comment on your chances at grad school admissions.